Search results for "SECONDARY STRUCTURE"
showing 10 items of 106 documents
Experimental dynamic analysis of elastic-plastic shear frames with secondary structures
2003
Various experimental models are developed to study the influence of lightweight secondary structures on the dynamic response of elastic and elastic-plastic shear frames. Small-scale two-story model frames, with an elastic single-degree-of-freedom secondary structure attached, are considered for sinusoidal and random in-plane support excitation. Both elastic and elastic-plastic responses are recorded by varying the material properties of the columns of a distinguished floor. Parametric studies are performed by varying the secondary structure's fundamental frequency and damping. Experimental results are compared with those obtained by computational simulations. Experimental and numerical resu…
Functional characterization of Tat protein from human immunodeficiency virus. Evidence that Tat links viral RNAs to nuclear matrix.
1990
The processes of transcription and posttranscription are assumed to proceed in close association with the nuclear matrix. In this study we demonstrated that Tat, the trans-activating protein from human immunodeficiency virus type 1 (HIV-1), binds both to the TAR region of the nascent HIV mRNAs and the nuclear matrix with high affinity. Both North/Western blotting experiments and nitrocellulose binding studies revealed that Tat binds with an association constant (K alpha) of approximately 1 x 10(9) M-1 to the TAR segment of HIV RNA; binding of Tat to this sequence which is present between position 32 and 82 downstream from the TATA box was also confirmed by gel retardation assays. Binding of…
A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease
2015
A pseudogene, designated as "ps(5.8S+ITS-2)", paralogous to the 5.8S gene and internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA (rDNA), has been recently found in many triatomine species distributed throughout North America, Central America and northern South America. Among characteristics used as criteria for pseudogene verification, secondary structures and free energy are highlighted, showing a lower fit between minimum free energy, partition function and centroid structures, although in given cases the fit only appeared to be slightly lower. The unique characteristics of "ps(5.8S+ITS-2)" as a processed or retrotransposed pseudogenic unit of the ghost type are reviewed, wi…
Tension Causes Unfolding of Intracellular Vimentin Intermediate Filaments
2020
Intermediate filament (IF) proteins are a class of proteins that constitute different filamentous structures in mammalian cells. As such, IF proteins are part of the load-bearing cytoskeleton and support the nuclear envelope. Molecular dynamics simulations show that IF proteins undergo secondary structural changes to compensate mechanical loads, which is confirmed by experimental in vitro studies on IF hydrogels. However, the structural response of intracellular IF to mechanical load is yet to be elucidated in cellulo. Here, in situ nonlinear Raman imaging combined with multivariate data analysis is used to quantify the intracellular secondary structure of the IF cytoskeletal protein viment…
Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain.
2019
Summary TRPML2 is the least structurally characterized mammalian transient receptor potential mucolipin ion channel. The TRPML family hallmark is a large extracytosolic/lumenal domain (ELD) between transmembrane helices S1 and S2. We present crystal structures of the tetrameric human TRPML2 ELD at pH 6.5 (2.0 A) and 4.5 (2.95 A), corresponding to the pH values in recycling endosomes and lysosomes. Isothermal titration calorimetry shows Ca2+ binding to the highly acidic central pre-pore loop which is abrogated at low pH, in line with a pH-dependent channel regulation model. Small angle X-ray scattering confirms the ELD dimensions in solution. Changes in pH or Ca2+ concentration do not affect…
Correction to ‘Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy’
2021
The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-un…
An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a β-barrel metalloprotein
2005
The unfolding process of the blue copper protein rusticyanin (Rc) as well as its dynamic and D(2)O/H(2)O exchange properties in an incipient unfolded state have been studied by heteronuclear NMR spectroscopy. Titrations of apo, Cu(I), and Cu(II)Rc with guanidinium chloride (GdmCl) show that the copper ion stabilizes the folded species and remains bound in the completely unfolded state. The oxidized state of the copper ion is more efficient than the reduced form in this respect. The long loop of Rc (where the first ligand of the copper ion is located) is one of the most mobile domains of the protein. This region has no defined secondary structure elements and is prone to exchange its amide p…
Temperature-controlled release by changes in the secondary structure of peptides anchored onto mesoporous silica supports
2014
Changes in the conformation of a peptide anchored onto the external surface of mesoporous silica nanoparticles have been used to design novel temperature-controlled delivery systems.
Oligonuclear Ferrocene Amides: Mixed‐Valent Peptides and Potential Redox‐Switchable Foldamers
2010
Trinuclear ferrocene tris-amides were synthesized from an Fmoc- or Boc-protected ferrocene amino acid, and hydrogen-bonded zigzag conformations were determined by NMR spectroscopy, molecular modelling, and X-ray diffraction. In these ordered secondary structures orientation of the individual amide dipole moments approximately in the same direction results in a macrodipole moment similar to that of α-helices composed of α-amino acids. Unlike ordinary α-amino acids, the building blocks in these ferrocene amides with defined secondary structure can be sequentially oxidized to mono-, di-, and trications. Singly and doubly charged mixed-valent cations were probed experimentally by Vis/NIR, param…
Redox-responsive organometallic foldamers from ferrocene amino acid: Solid-phase synthesis, secondary structure and mixed-valence properties
2011
Oligoferrocenes Fmoc-Fca(n)-OMe (n=3-5) are assembled in a stepwise precise manner from Fmoc-protected ferrocene amino acid Fmoc-Fca-OH (H-Fca-OH = 1-amino-1'-ferrocene carboxylic acid; Fmoc = 9-fluorenylmethyloxycarbonyl) via amide bonds on solid supports by sequential Fmoc deprotection, acid activation and coupling steps. The resulting well-defined oligomers form ordered zigzag structures in THF solution with characteristic hydrogen bonding patterns. Electrochemical experiments reveal sequential oxidations of the individual ferrocene units in these peptides giving mixed-valent cations. Optical intervalence electron transfer is detected by intervalence transitions in the near-IR.